Displaying 20 results from an estimated 3000 matches similar to: "exporting s3 and s4 methods"
2009 Jul 03
2
bigglm() results different from glm()
Hi Sir,
Thanks for making package available to us. I am facing few problems if
you can give some hints:
Problem-1:
The model summary and residual deviance matched (in the mail below) but
I didn't understand why AIC is still different.
> AIC(m1)
[1] 532965
> AIC(m1big_longer)
[1] 101442.9
Problem-2:
chunksize argument is there in bigglm but not in biglm, consequently,
2009 Mar 17
2
bigglm() results different from glm()
Dear all,
I am using the bigglm package to fit a few GLM's to a large dataset (3
million rows, 6 columns). While trying to fit a Poisson GLM I noticed
that the coefficient estimates were very different from what I obtained
when estimating the model on a smaller dataset using glm(), I wrote a
very basic toy example to compare the results of bigglm() against a
glm() call. Consider the
2007 Jan 22
1
Example function for bigglm (biglm) data input from file
This is to submit a commented example function for use in the data
argument to the bigglm(biglm) function, when you want to read the data
from a file (instead of a URL), or rescale or modify the data before
fitting the model. In the hope that this may be of help to someone out
there.
make.data <- function (filename, chunksize, ...) {
conn<-NULL;
function (reset=FALSE) {
if
2009 Apr 03
1
bigglm "update" with ff
Hi, since bigglm doesn't have update, I was wondering how to achieve
something like (similar to the example in ff package manual using biglm):
first <- TRUE
ffrowapply ({
if (first) {
first <- FALSE
fit <- bigglm(eqn, as.data.frame(bigdata[i1:i2,,drop=FALSE]), chunksize =
10000, family = binomial())
} else {
fit <- update(fit,
2011 Jan 10
1
debug biglm response error on bigglm model
G'morning
What does the error message "Error in x %*% coef(object) : non-
conformable arguments" indicate when calculating the response values
for
newdata with a model from bigglm (in package biglm), and how can I
debug it? I am attempting to do Monte Carlo simulations, which may
explain the loop in the code that follows. After the code I
have included the output, which shows that
2004 Jan 08
3
S3, S4, namespace
I have encountered an issue which I have been unable to resolve, involving
an S3 generic (print) being declared S4 generic in a package, and the method
being exported. This all works fine - the problem occurs when I try to
import the method to another package.
Here is the bit that works fine. -------------
#the .r file for package bar
2010 Jul 02
2
unable to get bigglm working, ATTN: Thomas Lumley
I am using an example posted in this help forum to work with a file. the head
of the file looks like:
988887 2007-03-05 2007-06-01 90 3 5.450 205500.00 999.00 999.000 0.000 0 0
988887 2007-03-06 2007-06-01 90 3 5.450 205500.00 999.00 999.000 0.000 1 0
988887 2007-03-07 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100 2 0
988887 2007-03-08 2007-06-01 90 3 5.450 205500.00 999.00 999.000 -0.100
2011 Feb 08
1
Fitting a model with an offset in bigglm
Dear all,
I have a large data set and would like to fit a logistic regression
model using the bigglm function. I need to include an offset in the
model but when I do this the bigglm function seems to ignore it.
For example, running the two models below produces the same model and
the offset is ignored
bigglm(y~x,offset=z,data=Test,family=binomial(link = "logit"))
2007 Jun 29
1
Comparison: glm() vs. bigglm()
Hi,
Until now, I thought that the results of glm() and bigglm() would
coincide. Probably a naive assumption?
Anyways, I've been using bigglm() on some datasets I have available.
One of the sets has >15M observations.
I have 3 continuous predictors (A, B, C) and a binary outcome (Y).
And tried the following:
m1 <- bigglm(Y~A+B+C, family=binomial(), data=dataset1, chunksize=10e6)
2009 Feb 19
1
Questions about biglm
Hello folks,
I am very excited to have discovered R and have been exploring its
capabilities. R's regression models are of great interest to me as my
company is in the business of running thousands of linear regressions
on large datasets.
I am using biglm to run linear regressions on datasets that are as
large as several GB's. I have been pleasantly surprised that biglm
runs the
2015 Jun 15
2
Regresión logística
Hola,
estoy intentando hacer una regresión logística entre la primera columna de
mi data.table (In.hospital_death) y otras dos (GSV y BUN) , me da el error
de abajo, he intentado eliminar las filas con valor NA por si esta función
no lo admite, pero sigue dando el mismo error. ¿Alguien sabe porqué ocurre?
(probé previamente a usar la función glm pero obtenía out of memory)
library(XLConnect)
2007 May 03
1
Imports/exports of S4 methods
I have a question about what to do in the following situation (please bear with
the setup):
Package A defines an S4 generic 'foo' and as well as S4 methods for 'foo' and has
exportMethods("foo")
in its NAMESPACE file.
Package B defines another method for 'foo' for class "bar" and has
importFrom(A, "foo")
exportMethods("foo")
2007 Feb 12
0
predict on biglm class
Hi Everyone,
I often use the 'safe prediction' feature available through glm().
Now, I'm at a situation where I must use biglm:::bigglm.
## begin example
library(splines)
library(biglm)
ff <- log(Volume)~ns(log(Girth), df=5)
fit.glm <- glm(ff, data=trees)
fit.biglm <- bigglm(ff, data=trees)
predict(fit.glm, newdata=data.frame(Girth=2:5))
## -1.3161465 -0.2975659
2008 Jun 08
1
R CMD CHECK WARNING inappropriate for S4 method?
The package 'graph' defines classes graph and graphNEL (extending
graph) and a union,graph,graph-method. These are all exported and
fully documented.
The package 'GSEABase' Imports: graph and importClassesFrom(graph,
graphNEL). GSEABase defines methods on union for its own classes (not
graph / graphNEL), and has exportMethods(union).
union,graph,graph-method is not used in
2007 Aug 16
4
Linear models over large datasets
I'd like to fit linear models on very large datasets. My data frames
are about 2000000 rows x 200 columns of doubles and I am using an 64
bit build of R. I've googled about this extensively and went over the
"R Data Import/Export" guide. My primary issue is although my data
represented in ascii form is 4Gb in size (therefore much smaller
considered in binary), R consumes about
2003 Sep 05
1
namespaces and S4 methods/classes
The current version of the methods package now has a namespace. Packages
using S4 methods and classes can have NAMESPACE files. New directives
can be included in NAMESPACE files to import and export classes and
methods.
Namespaces allow cleaner definition of the API for packages, and are
needed for future improvements to R.
NOTE: This is a major revision. In principle, it should be back
2013 May 08
1
Namespace/inheritance problem in S4 methods for a union class
Hi,
I started this post on bioc-devel but this seems to be more general:
https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html
See reproducible example from Martin below.
Thank you.
Renaud
---------- Forwarded message ----------
From: Martin Morgan <mtmorgan at fhcrc.org>
Date: 7 May 2013 19:55
Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem
in S4
2010 Jun 16
0
biglm.big.matrix: Problem with weighting
Hello colleagues,
I have tried to use the package bigmemory, biganalytics and biglm. I
want to specify a multivariate regression with a weight.
I have imported a large dataset with the library(bigmemory). I load the
library (biglm) and specified a regression with a weight. But I get
everytime an error message like "object not found" or "`weights' must be
a
2012 Jan 03
0
Biglm source code alternatives (E.g. Call to Fortran)
Hi everyone,
I have been looking at the Bigglm (Basically does Generalised Linear Models
for big data under the Biglm package) command and I have done some profiling
on this code and found that to do a GLM on a 100mb file (9 million rows by 5
columns matrix(most of the numbers were either a 0,1 or 2 randomly
generated)) it took about 2 minutes on a linux machine with 8gb of RAM and 4
cores.
2012 Mar 30
3
ff usage for glm
Greetings useRs,
Can anyone provide an example how to use ff to feed a very large data frame to glm?
The data.frame cannot be loaded in R using conventional read.csv as it is too big.
glm(...,data=ff.file) ??
Thank you
Stephen B